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Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with inhibitor L97 and L-proline at 1.97 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7F9T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1 M Amino acids (0.2M DL-Glutamic acid monohydrate, 0.2M DL-Alanine, 0.2M Glycine, 0.2M DL-Lysine
monohydrochloride and 0.2M DL-Serine) 0.1 M Buffer (Sodium HEPES, MOPS), 30 % v/v Precipitant (40% v/v Glycerol, 20% w/v PEG 4000)
Crystal Properties Matthews coefficient Solvent content 2.54 51.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.733 α = 90 b = 73.644 β = 111.38 c = 74.906 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2019-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.97 60.64 98.6 1 10.7 6.9 40410
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2.01 97.9 0.4 0.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7F9T 1.973 52.682 1.34 39532 1981 96.45 0.177 0.1748 0.1799 0.2174 0.2205 54.3235
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3906 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 81
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction autoPROC data reduction autoPROC data scaling PHASER phasing